About this Research Topic
The processes that underpin functional redundancy (FR) are yet to be discovered. To understand functional redundancy, researchers must provide a fair understanding of the mechanisms ruling positive interactions within the microbiomes, which require direct or indirect physical contact between the microbial community members. These mechanisms can be categorised into a) Horizontal gene transfer (HGT), b) Cross-feeding, and c) Quorum Sensing. The positive interactions (+/+) can increase interdependencies and lead to poor microbial connectivity and less diverse microbiomes than antagonistic (+/-) interactions. However, the relevance of antagonism on functional redundancy is also not known in detail. In this respect, Molecular Omics approaches and metabolic computational models can contribute to understanding microbial interactions in microbial ecology.
The dynamic flow of genes via horizontal gene transfer (HGT) across microbial lineages contributes to the stability of the functional genes in different communities under stress despite their distinct taxonomic compositions. The FR of microbiomes under disturbance might be due to direct interaction between the community colonies and indirect physical contact mediated by the exchange of chemical and metabolic secretions. Even though considered the “currency” of microbial interactions, the metabolites exchanged among the complex microbiomes are also understudied. For example, we need to understand the functional state of a microbiota by predicting what metabolites were secreted, consumed and exchanged via a network of multi-level trophic cascade interactions (cross-feeding). With omics technologies and available computational predictive modelling frameworks, it is now possible to predict, quantify and validate microbial metabolic abilities based on genome composition and gene content. Therefore, moving from the descriptive taxon scope to a more function-oriented phase in microbiome research is necessary to unravel complex molecular microbe-microbe interactions. To this end, computational modelling from the molecular level (fine-grain) to the system level (coarse-grain) can be implemented to shed light on molecular mechanisms, which can then be validated/refined empirically using various novel experimental techniques.
The main goal of this Research Topic is to Integrate Experimental and Computational Approaches to reach a clear definition and understanding of the functional redundancy underlying taxon-function decoupling patterns broadly identified in microbial ecosystems under natural versus anthropogenic conditions.
Keywords: Taxon-function decoupling, functional redundancy, Omics, cross-feeding, metabolic prediction, microbe-microbe networks
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